Use sticky traps to catch the flies near your apple tree. Hang the traps on the branches of your tree. The flies will be caught on the sticky adhesive of the trap. Replace the traps whenever the stickiness wears off or the traps become filled with flies.
Spray the apple tree with an insecticide to keep flies away from your tree. Insecticides are most effective when used during late June to October. This is the period when the fruit flies have the most activity.
Spray dormant oil on your tree just before the tree begins to bud. The oil will kill any eggs on the tree. You should apply the oil during early spring.
Plant Butterfly Weed plants around your apple tree. Butterfly Weed contains a natural parasite that kills fruit flies without harming your apple tree.
Place bags over the apples to cover and protect them. Staple the opening of the sandwich bag around the fruit. Cut a small sliver in the bottom corner of the bag to allow the apples to drain.